No Longer Four
by EbbieBlack
Summary: AU set after the third movie. Once four brothers traveled back through time to retrieve their friend. But in the end only one of the brothers returned with their friend. Now the three brothers have returned home and although only a year passed for them...
1. 13 years

Chapter One - 13 Years Later

Lightening streaked across the sky as a crack of thunder chased it. But the lone figure that stood atop the roofs paid it no mind nor did he heed to the rain that the night threatened him with. His eyes scanned the darkness that stretched out before him, covering the city that had been his home for nearly thirty years. It was his domain, his to protect and for the last twelve years he had done so alone.

He knew for a time that the evil he fought every night had been winning. The cold metal that was now his right hand was a reminder and proof of that, but the balance was starting to shift back.

Another flash and this time the thunder boomed causing him to finally look up at the night sky with an unimpressed glance. He had once long ago enjoyed being topside during a storm. The smell of rain on the air, wild winds and watching as Mother Nature reminded the city that she was still the dominant one and could wipe them away if she wanted. But now it was a reminder of things… _of people_… best forgotten. Because there was no changing the past, no rewriting history… _no bringing people back_…

Roughly shaking his head to rid himself of those particular thoughts and people. There was no point in them.

This time when the thunder cracked, he knew it was time to go. Moving like a shadow, he leapt across the rooftops, but as he moved those thoughts he had pushed away came back…

"_Hey, guys … I'm not going back."_

A light sweat broke out on his skin; panting slightly as he pushed himself to go faster. The mere memory still made him feel sick. He would later realized part the feelings racing through him in the moment Mike had said he was staying came from the realization of going back without one of his brothers. But another part … and, if he was honest with himself, the largest part … came from the fact that it wasn't just any brother. No, it was _Michelangelo_. Mikey, his little brother and best friend. The one who would hide out with him as they waited out the wars Leo and Raph raged against each other.

_He had turned to his slightly older brother, knowing he would be the one to set Mikey straight. _

"_I been thinkin' the same thing, Leo. People appreciate us here. We don't have ta live like moles."_

His discomfort kicked up a notch and he ran even faster has though he could out run these memories.

In desperation he turned to his eldest brother. His _responsible_ brother. His last hope.

"_Actually…"_

But in the end even Leo had let him down.

_Then, as Raphael would say, turtle luck was running true to form for the scepter began glowing and spinning._

Gasping for air, April's words… her last desperate attempt to convince them to go back… rang in his ears…

"_You can not split up. You're brothers."_

He broke out into a full out sprint to escape; running away from them. He didn't want to remember what happened next…

What he realized next…

_He was the only one who wanted to go back to New York, and that meant … his brothers didn't care. They didn't care if he was there. They didn't care if they were separated. They didn't … they didn't—_

He stumbled and fell to his knees. Tears leaking out of his tears, no matter the determination he had to hold them back; to not let them fall…

His heart pound as those it would explode his chest tightened with pain… anger… resentment… fear.

_The decision on his brothers' faces was telling. It hadn't mattered what either he or April had said. It had not mattered what Mitsu had said to Mikey. They were staying…_

And they hadn't cared that he wasn't.

"AAAAAAAAHHHHHHHHHHHHHHH!"

He threw his head back and let out an inarticulate roar of anger and grief. The anger took over his body as he lashed out whatever was closest. Vent shafts were dented an ripped from their settings to pay for his brothers' crime… The wooden rooftop shed had holes punched in its walls, its door splintered into pieces.

When the destructiveness had passed the grief took hold. He could still see in his mind, his father's face when only he and April returned. The look of devastation and grief had marred his master's until his death.

Because on the one year anniversary of his return (his brothers' abandonment of them), he father passed away.

He had not been enough to keep his father around. He alone was not enough reason for his father to keep wanting to live. And that hurt as much if not more than his brothers choosing to remain in feudal Japan without him.

With great difficultly he shoved those memories back into the darkest places of his mind.

He stood on shaking legs, bracing himself on the ledge of the roof. He felt alone in the world.

And in the truest sense of the word, he was alone; the last of his kind, the last of his species.

But in another way, he wasn't. He still had family. Just not the one he wanted; the one he had grown up with.

He closed his eyes, and focused on making his mind go blank. He knew with all the noise he had made, he needed to leave before he was discovered. Descending on a nearby fire escape, he was able to get his breathing and heart back under control.

When he reached the alleyway below, he cast on last look up at the night sky. He had wished, once long ago, that things could be different…

That he could freely visit his friends and honorary 'neices and nephews'…

That his father was still alive…

That his brothers had come back with him…

That his brothers would come now…

But those days passed just a few weeks after his father died. As had the days where he could dream and make wishes.

His brothers had seen to death of those things.

His anger would have to wait until tomorrow night, the anniversary of his family's abandonment of him. And tomorrow when he allowed the thoughts of his brothers and father to come to mind and fuel his anger, than he would unleash it on the thugs and criminals of New York and they would pay the heavy price for that anger.

Because tomorrow night, it would not be the Phantom the darkness needed to worry about…

It would the once gentle and peaceful turtle that would wear the gear of his youth and the purple bandana his father and master had given him nearly twenty-five years ago…

For one night those that plagued the night would fear the name…

Donatello.


	2. Chapter 2

_**Sorry about the lateness of this chapter, but thanks to my wonderful laptop that decided its' screen wasn't going to work and the battery that now never wants to hold a charge again, I lost everything I had typed up for this story as well as 'Changed' and 'Waiting'. Then when I finally get this chapter typed up, our internet goes down. So I am currently posting this from at my grandma's house.**_

_**Ok, my little rant is done, I feel better and I hope this chapter lives up to expectations.**_

_**Again, I own nothing but my OCs, that you will meet in later chapters. Enjoy.**_

**Chapter Two: A Year in the Past**

_Loud angry voices that had been muffled became clear and understandable as the door creaked open. The voices were muffled again as the door was closed as softly as it had been opened. The room remained silent, except for the soft padding of feet and the occasional sniffle as a small figure crossed the room and climbed up onto the bed to sit beside his brother, who had tossed the blanket backing invitation when the door had closed._

_He felt arms encircle him once the blanket was settled over his legs; his own arms wrapped around his brother. The comfort was instantaneous when he tucked his head under his brother's chin._

_One arm moved away to pick-up a book off the small nightstand that sat beside the bed,_

"_Which story would you like to hear Mikey?"_

--

Mike's eyes snapped open as he rolled onto his shell. Stretching his arms above his head, he took a moment to think about the dream… well, memory actually… he realized. Like so many others he had had recently, this one was about Donnie and himself.

Rolling back over, he saw that both Raph and Leo were already up and had been for some time if the dirty breakfast dishes were any indication.

He stood slowly, stretching once more as he crossed the room to stoke the fire back up. He never knew just how cold it could get in Japan.

As he got the fire going again and took a moment to warm himself beside it, he began watching the embers drifting up, his thoughts seem to drift right along with them… he wondered what Don was doing… what their friends might be doing… how Splinter was doing… but as suddenly as the thoughts came, reality reared it's head and shoved them away. Technically, none of them were alive yet. There was no mutant turtle named Donatello living in the sewers of New York City with their mutant rat father, Splinter. There was no Casey Jones busted punk heads, no April O'Neil reporting for Channel 3, no Keno delivering pizza in New Work City. There wasn't even a New York, much less a New York City yet.

None of the people he called family in NYC were alive yet…

…and wouldn't be for over 480 years yet.

He shook his head to clear these thoughts away. It didn't do any good to dwell on them anyways. They had made their choice to stay and _good_ or _bad_, that's the way it was.

But moments like this always caught him off guard and he would wonder if it had been the right one.

Scooping up some of the leftover porridge from his brother's breakfast in a small bowl to eat on the way and grabbed the remaining cloak from beside the door on his way out to find his older brothers.

As he walked along the path that wound its' way through the woods to a small clearing they used for training and sparring, his thoughts drifted back over their year here.

They had made the decision to stay in the heat of moment. There had been no time to discuss staying, to talk them out of it. None of them had shared their feelings about staying or why they wanted to stay. Until that moment.

He had made the choice to stay because of his feelings for a girl who would never return them and already loved someone else.

Raph had made his choice based on the feelings invoked by one small boy, who wasn't afraid of him or afraid to touch him without flinching.

Leo chose to stay because two of his brothers had already made up their minds to stay and because of the feeling he got from the people here when he walked in the open. There was no screaming or running in fear when they saw him. No, they would wave or smile. Some even greeted or spoke to him.

Not yet realizing the challenges and difficulties that they would have to face. Not fully what they had gotten them selves into. Nor understanding what staying and what this choice meant for their lives.

They had had to build their own home, grow or gather their own food, clothing and supplies had to be made or traded for. But they had done it and what had they gotten out of the deal…

Walking in the sunshine…

Open meadows and forests to play and train in…

Long, flowing, clear streams to swim in…

A seemingly endless blue sky…

Fresh, clean air to breathe…

Being able to see the sun rises and set…

'_At what cost?'_ a voice whispered in his head.

That made him pause. It was not the first time this particular thought had crossed his mind nor was it the first time he had heard this voice. In fact, they had been there a matter of weeks when it happened for the first time.

Sure they had given up:

Heat and air conditioning.

Running water and electricity.

Indoor plumbing.

And all the other conveniences of the twentieth century were right at the top of the list, but…

'_How about __who__ it cost you?'_

Well… there was April & Casey, Keno…Danny, but they had made new friends here as well. Friends like: Yoshi, Mitsu, Kenshin…that Honor guard dude Benkei…

'_Try again.'_

He knew who the voice was talking about. The thing was… he didn't want to think about them. When he did all he can see is his brother's face when he said he was staying.

The disbelief in his eyes as Leo and Raph declared they were staying as the wind picked up and the time scepter began to grow brighter.

The pain that flashed in them as he & April disappeared and Kenshin & Benkai appeared.

By the time he had gotten to the clearing, he was able to push those thoughts to the back of his mind. But all thoughts left his mind any ways as he crossed to his brothers, confusion taking their place in his foremost thoughts.

Raph was holding some sort of wooden object in his hands that they were both examining. As he got closer he could make out strange symbols carved in it and he also realized that the symbols could be turned,

"Hey, what'd ya got there Raph?"

"A puzzle box." Raph replied without even looking up. His attention completely on the object in his hands.

"Yoshi brought it to him this morning," Leo answered Mike's silent question as he continued to study the box in Raph's hands, "his grandfather said that, _if the legend is true_, that puzzle box belonged to one of the Kappa that defeated Lord Norinaga's ancestors those many years."

"Cool. He say how to unlock it?"

"No."

"Oh."

Silence fell again as Leo and Mike watched Raph mess with the puzzle. After maybe ten minutes, he sighed and tossed it to Mike,

"Here you try." He grumbled, "I'm goin' back to training. Ya comin' Leo?"

He gave his brother a nod, before following. Mike took a moment to get a closer look at the 'puzzle box'.

'Hmmm…let's see there are twelve rotating dials and 1, 2, 3… 8 symbols on each dial. Huh.' He noticed that two of the dials seemed to be stuck,

"Must be jammed or somethin'," he mumbled to himself. As he turned the dials, he thought there was something familiar about the pattern the symbols would make when lined up next to certain other symbols.

'What is it?' he almost had it…

"Hey, Mike!"

"What?" he yelled back, looking up to see what Raph wanted.

"We're gonna go fer a swim. Ya comin'?"

"Yeah, I'm comin'."

He continued to fiddle with the puzzle as he followed behind his brothers. It was just before they reached the small waterfall and lagoon where Raph, Leo and… where Raph and Leo had met Mitsu, that Mike figured why the pattern looked familiar,

"Hey guys, look at this."

Leo and Raph turned back to see what their little brother found.

"They symbols make letters. Look." He passed the puzzle back to Raph as Leo looked over his shoulder.

Sure enough, Mike had made the letters,

'|\|' and '\/\/'

"Odd that an ancient Japanese puzzle box would make English letters," Leo said.

"Could be a coincidence, ya know," Raph shot back as he turned some of the other dials to see what other letters it could make.

Mike stepped to Raph's other side as the red-banded turtle began rotating the dials, not realizing that as he made letters on one side, on the opposite side a word was forming.

When he noticed that some of the dials were locking in place, he started turning the puzzle over. He noticed on the one side an '|-|' and '|\/|' were formed with the stuck dials, but Mike grabbed it out of his hands before he could do anything else,

"HEY!"

Mike ignored him, quickly turning and locking the remaining letters in to place using the last five dials,

"Solved it" he cried, quickly tossing it back to Raph before his brother could grab him.

"HOME" Leo read out loud.

It was then the ground began to shake… the wind began howling and swirling around them faster and faster…

And then, in a flash of light…

They disappeared.


	3. Chapter 3

_He walks the night. _

_Alone. Restless. Ready. _

_Clad in black, masked, he was a shadow among shadows, a whisper among the murmurs and mumbles of the dark. Night after night, clothed in black, mask covered face, he stalks the wild, dark streets. Because the only thing that seems to keep the demons inside him at bay are taking out the real-life demons that came out at night._

_They call him Phantom and he is everywhere._

"I still can't believe that you actually wrote this crap. I mean '_Unknown, unseen, unwanted, he stalks the hunters in the steaming jungle that is the city.'_ where the hell did you come up with that? Talk about over dramatic Pennington."

"You're just sore you didn't think of it first." came a muffled reply from the kitchen.

"Pfft, whatever kid." Casey Jones shot back. A small smile showing on his face as he leafed through the book. Still amazed at what the scrawny punk had done and the man he had turned into.

"You seen him lately?" he asked, as he tossed the book onto the coffee table and accepted the bottle held out to him.

Casey studied the younger man next to him. Danny Pennington. He met the kid through unbelievable circumstances. At one time they stood on opposite sides of a growing problem, but connected and changed through the strange family that brought them together in the first place. He had watched the little punk grow into a bigger punk, then a man who stood against his father to enlist and become a marine. The adopted little brother who learned about engines from him, who Dan grieved with when he lost childhood friends and brothers in arm; who had grieved with him when he lost Karen and helped him climb out of the black he found himself in after; helped him raise his children and celebrate every special occasion since.

"No, but then it is that time of year." Dan answered as settled into the recliner. Both let the silence stretch out, lost in own thoughts, but both were thinking about the same thing.

Casey knew that things were gonna change when April and Don came back with out the other guys. He just hadn't realized how much. Donnie wasn't the techno-goofball anymore and he and Splinter were hardly ever in contact with anyone topside. Then on the one year mark, Don had called and said Splinter had past and if he would let April, Keno, Danny, and Professor Perry know.

A week after the funeral, Casey had gone to visit Don, only to find the lair boxed up and a letter asking Casey to store everything until Don came back.

Almost two years would pass before they would see him again.

"He'll probably stop by later next week, if not this weekend. Promised he would see the tape Ry made on his class trip to the museum."

Dan nodded, rising to grab another beer and bring another back with him for Case.

"Gonna enjoy the quiet with them at your mom's for the weekend?"

"Probably not. I'll end up turning on something in every room." Casey admitted with a grin just as his cell rang. He headed to front of the house as Dan cleared the take-out containers and empty bottles from the coffee table. With clean up out of the way, he took a moment to study the man that had become a strong presence in his life.

Casey Jones was part friend, part big brother, and even part father to him. He kicked his butt when it needed kicking and some times when it hadn't. He took him in and stood beside him when his own father had thrown him out when he told him he was joining the Marines after graduation. They had stood together when Dan buried old friends and fellow Marines. He stood by Casey when April left and when he buried Karen, his wife, three years ago. He moved in to help with the kids and then moved across the street when Casey got his life back together.

A short series of taps on the kitchen window caught his attention. A glance over his shoulder didn't reveal anyone or anything there, but as soon as he turned away he heard them again. Thinking it was some neighbor kid fooling around, he eased off to the side so no one looking in could see him. When the taps came again he opened the window trying to grab whoever was out there, only to have his arm twisted behind his back as he was pulled half out the window. His free hand tried to grab the window frame, but he soon found himself face first against the side of the building half in, half out the window.

"Thought you were a Marine Pennington." a soft gruff voice rumbled out of the darkness.

Dan quit struggling the second he heard the voice,

"Hey Don, long(grunt) time no see…"

His arm was freed and he felt himself being pulled up and pushed back inside. He staggered a little to regain his balance as a figure jumped in behind him and closed the window,

"Took you long enough to let me in. Waiting for the neighbors to catch a glimpse of me."

Before Dan could shoot back a comment a pungent odor caught his attention,

"What the hell Don, you reek!"

"Yeah, well you wouldn't smell like sunshine and daisies after swimmin' in the Hudson either." Don shot out as he pulled off his bandana. He rung it out before draping it over the faucet.

"Why were you in the Hudson?" Dan asked from behind the hand he had clamped over his nose and mouth as he watched Don pull out all of his little gadgets.

"Interrupted a CD robbery and found out they had a meeting with the Foot. Apparently De la Vario been meeting up with the Foot, with Itachi running it, Dragons crashed and then the cops showed. It was either get through them and make the 10 o'clock news or go for a swim. Figured I wasn't dressed to be on the news."

He caught the towels Dan threw at him and left his gadgets drying on the counter and his phantom gear in the sink,

"I'll get that stuff later, gonna use the shower."

He headed down the hall before Dan could say anything. The bathroom closed just as Dan left out a small laugh.

"Hey Dan who ya talking to back here?" Casey asked.

"Give you one guess" he replied, gesturing to all the gadgets and gear.

Cranking the hot water on, he let the shower run as he unlocked and removed the metal limb that served as his right hand. Tapping it against the sink a couple times as his mind was lost in thought before setting it to the side on the hand towel. He braced himself against the sink on his left hand and stared at himself in the mirror, not seeing his reflection but reliving the meeting he had crashed.

The fact that the Cobra Diablos were meeting with the Foot was trouble, but the fact that Itachi was representing the Foot and that Karai apparently not knowing anything about the meetings were what was bothering him the most. Although The CDs' had only been around for the last five or six years, they had grown quickly and had become a bigger problem than the PDs' ever were.

With a sigh he turned and entered the shower, braced against the wall, he simply let the water beat down against his head and shoulders for a few minutes. He was exhausted, sore and sick of how his life was going. Between the small time muggers, wanna be thieves, and regular crooks his nights were packed, but then you add in the PDs, CDs, and Foot and it made for one exhausted crime fighter.

With a tired sigh he turned the water down from scalding to hot and set to work on not smelling like week old garbage left to rot in the sun.

In the end he used up the bottle of Casey's body wash as well as a bar and a half of soap. He mentally thanked Casey or Danny for the sweats that were sitting on the counter waiting for him. They both knew how he felt about his scars and although he grew up not wearing clothes, now he felt uncomfortable because he figured all anyone saw were those scars.

This time when he looked in the mirror he saw himself. His left hand automatically going to his right shoulder; the discolored massive burn scar that ran half way to toward the locking mechanism implanted in his arm and half along his collar bone.

It was one scar that he could never regret and never forget how it came to be. As his finger ran over it…

_He could smell the smoke that choked the air in the building as he raced up the stairs. He heard their terrified screams as he used his shoulder to open the door. Burning splinters imbedding themselves in his flesh. He can taste the blood in his mouth as he bites his tongue and uses his shoulder to move the burning beam out of the way. He could see…_

"Don you ok?"

Shaking his head, he didn't answer as he pulled the black hoodie on and opened the door,

"'m fine." he brushed past Dan, heading back to the kitchen.

"Donnie, long time no see." Casey said as he caught sight of his long time friend. When Don just grunted at him, he held out a bottle,

"You look like you need a drink."

He held his breath for a few seconds before letting it out and relaxing. He gave Case a small smirk as he took the offered bottle,

"Thanks Case-man. Its good to see you." before the three of them headed back into the living room.

* * *

_Meanwhile…_

Deep under the city something was happening. Dust and dirt began swirling round and round; streaks of lights were appearing again and again; the area seemed to hum with energy and with flash of light three figures seemingly fell from no where to land atop each other.

As suddenly as it had all began, it was over.

The dust settled, the wind stopped and the area was plunged back into darkness for a moment before a few stray beams of moonlight shone in through a grate further down the tunnel.

A groan echoed through the station. Soft scraps and scuffles could be heard as though someone was moving about.

"Ooowww my head" a voice whined.

"Shud up Mike" a gruff voice order.

"Both of you quiet" a third voice order, "We don't know where we are or if there is anyone else nearby that could hear us."

Both the other voices grumbled and mumbled as they freed themselves from the pile they had fallen into. Their eyes adjusting to the semi-darkness after a couple of minutes past.

"Wait here, I'm going to go check out that light." a voice order.

"Whatev' Leo, I ain't waiting around, let just go." a gruff voice answered.

A lifetime of training had them melting into the shadows even as they moved towards the light. Problem was, you couldn't stay in the shadows and look up into the light.

A siren broke the silence of the night, followed by the screech of a cat and the clattering of trash cans.

"We're back."

Mike stepped out into the moonlight as he gazed up at the world above. They were back in New York.

"But how…?" he asked without looking away.

"It must have been that puzzle box." Leo answered as he moved next to his younger brother, still remaining half in the shadows.

Raph remained in the shadows, not wanting to believe what had happened. He had been happy in Japan and now they were back living like moles and hiding from the world. So lost in his mind, he didn't notice right away when Leo spoke to him,

"Raph, come on. We need to find Splinter and Donnie." Leo said once he finally got brother's attention back. Without waiting for a response, he turned and headed further down the tunnel, looking for a manhole cover. In order to find the lair, they had to know where they were.

After a quick trip topside, Leo found they were two miles South of the lair. But the quick recon trip up had Leo also realizing something wasn't right and rather than take a chance running across the roofs, they stayed in the sewers.

But after only a half mile, the Raph and Mike also found that something wasn't right as they kept running into dead ends, closed off tunnels and new tunnels that had been there before they left to retrieve April.

But the biggest shock came when they finally arrived at the lair or at least what used to be the lair.

Because they knew instant they climbed down the ladder that they would not find their father and brother here.

Leo found the power box and quickly turned the power on. Only three of the lights above turned on, but it was enough to see that this place had been abandoned long ago.

The train cars had collapsed in on themselves, only one remained partially standing. Dust covered everything. There were no obvious signs that anyone was there or that anyone had even ever been there.

Mike was the one to realize that all of their stuff was gone,

"Dudes, there's nothing here." Mike's voice was soft as looked to his oldest brother for answers.

"We'll have to head topside. There are no answers here." Leo said as he turned and headed back up the stairs. Raph followed behind after a moment. Mike was froze as he looked around what had been their home,

"Mikey, let's go." Leo called out.

As he walked past, he turned the power back off and the station was plunged back into darkness. He stopped at the top of the stairs and looked back over the darkness, just barely able to make out the outline of the last train car. With a sigh, he quickly climbed the ladder and raced to catch up to his brothers.

They remained in the sewers only long enough to find a manhole Leo deemed safe to exit out of. Then they were but shadows as they scaled the nearby fire escape and hit the rooftops.

"So what's the plan Leo?"

"We need information." Raph shot his older brother his '_are you seriously gonna just state the obvious_'.

"We already know tha' Leo."

"Uh, guys…"

"Look Raph I don't know what you"

"Guys"

"What we need at do is"

"GUYS!"

"What Mikey?" Leo snapped, finally noticing that Mike had his 'chucks out and had backed closer to him and Raph,

"We got company." was all that was said as Leo and Raph both drew their own weapons as they realized they were surrounded by who they soon recognized as Foot Ninja.

* * *

Don had stayed only long enough to drink his beer. Casey had already tossed his nasty smelling clothes into the wash and found an older set of phantom clothes. With the promise to come back later in the week, he suited back up and headed back out into the night.

For some reason as he ran across rooftops, his mind drifted and he soon found himself near the old lair.

He paused when he could hear the faint sounds of a nearby fight. It took him a few moments to locate the alleyway the fight was coming from. As he looked down trying to determine if he needed to step in, he noticed three shapes that looked like..

_'No it couldn't be. They were gone. They weren't real. It's just a trick to draw…_'

"MIKEY!"

"God Damn it!" he swore as he leapt over the edge into the fight below.

* * *

I'm sorry about the long wait on continuing my stories. I have most of the next chapter in 'Waiting' typed up and something started on the next chapter for 'Changed'. Not saying when they will be up though. I'll do my best to get them up soon, I hope.


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